Discovery and Evaluation of Small Molecule Inhibitors of the S100B-p53 Interaction

Abstract

S100B is a calcium-binding protein that is highly upregulated in malignant melanoma and is currently used as a prognostic indicator for the disease. S100B has been shown to bind to p53, decreasing p53 protein levels and inhibiting its function. Small molecule inhibitors are being investigated which use the S100B-p53 interaction as a therapeutic target, and the drug pentamidine was found to bind S100B; pentamidine-derived compounds were then designed, synthesized, and analyzed. Molecular Dynamics simulations of the pentamidine-S100B complex were performed in an effort to determine what properties would be desirable in a pentamidine-derived compound as an inhibitor for S100B. These simulations predicted that increasing the linker length of the compound would allow a single molecule to span both pentamidine binding sites on the protein. The resulting compound, SBi4211 or heptamidine, was synthesized and experiments to study its inhibition of S100B were performed. The 1.65 Å X-ray crystal structure was determined for Ca2+-loaded S100B bound to heptamidine and gives high-resolution information about key contacts that facilitate the interaction between heptamidine and S100B. Additionally, NMR HSQC experiments with both compounds show that SBi4211 causes perturbations in the chemical shifts of the same residues of S100B as pentamidine. SBi4211 is able to selectively kill melanoma cells with S100B over those without S100B, indicating that its binding to S100B has an inhibitory effect and that this compound may be useful in designing higher-affinity S100B inhibitors as a treatment for melanoma and other S100B-related cancers.